KazRNA-Pipe-GPU-Accelerated, Reproducible Nextflow Workflow for Integrated Bulk and Single-Cell Transcriptomic Profiling
TL;DR
KazRNA-Pipe is presented, an open-source Nextflow v26.6 workflow processing both bulk and single-cell RNA sequencing (RNA-seq) within a unified Singularity-containerized environment with graphics processing unit (GPU) acceleration through the RAPIDS ecosystem.
Abstract
Reproducible high-performance computing pipelines for transcriptomic analysis are essential for population-scale precision oncology, yet most published workflows address only a single sequencing modality or lack benchmarking on underrepresented populations. We present KazRNA-Pipe, an open-source Nextflow v26.04.6 workflow processing both bulk and single-cell RNA sequencing (RNA-seq) within a unified Singularity-containerized environment with graphics processing unit (GPU) acceleration through the RAPIDS ecosystem. The pipeline was validated on 22 esophageal squamous cell carcinoma (ESCC) bulk RNA-seq samples from a Kazakhstan cohort (PRJNA608223) and on the largest public ESCC single-cell atlas (GSE160269). Quantification concordance across STAR, HISAT2, and Salmon reached Spearman ρ ≥ 0.90. BayesPrism deconvolution resolved cell-type proportions across all 22 samples.